error for QC

[Yang song]

I run the QC step as following:

kneaddata \

 --input   /local/scratch/ysong/wgs_virgina/SRS011269/SRS011269.denovo_duplicates_marked.trimmed.1.fastq --input /local/scratch/ysong/wgs_virgina/SRS011269

/SRS011269.denovo_duplicates_marked.trimmed.2.fastq \

   -db /local/scratch/ysong/Homo_sapiens_BMTagger_v0.1/  \

   --run-bmtagger  \

 --trimmomatic /usr/local/packages/trimmomatic/ \

 --bmtagger /usr/local/packages/bmtagger/ \

   --output /local/scratch/ysong/wgs_virgina/104_qc_output/SRS011269/ \

However, I got error about -extract

Initial number of reads ( /local/scratch/ysong/wgs_virgina/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1.fastq ): 5151653

 Initial number of reads ( /local/scratch/ysong/wgs_virgina/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.2.fastq ): 5151653

Running Trimmomatic ...

Total reads after trimming ( /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1_kneaddata.trimmed.1.fast

q ): 4700575

Total reads after trimming ( /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1_kneaddata.trimmed.2.fast

q ): 4700575

Total reads after trimming ( /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1_kneaddata.trimmed.single

.1.fastq ): 175662

Total reads after trimming ( /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1_kneaddata.trimmed.single

.2.fastq ): 211609

Decontaminating ...

Running bmtagger ...

Error executing: /usr/local/packages/bmtagger/bmtagger.sh -q 1 -1 /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_mark

ed.trimmed.1_kneaddata.trimmed.1.fastq -T /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1_kneaddata_p

aired_temp_V__1Bi --extract -b /local/scratch/ysong/Homo_sapiens_BMTagger_v0.1/Homo_sapiens_assembly19.fasta.bitmask -x /local/scratch/ysong/Homo_sapiens_B

MTagger_v0.1/Homo_sapiens_assembly19.fasta.srprism -o /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.trimmed.1

_kneaddata_paired_Homo_sapiens_assembly19.fasta_bmtagger -2 /local/scratch/ysong/wgs_virgina/104_qc_output/SRS014343/SRS014343.denovo_duplicates_marked.tri

mmed.1_kneaddata.trimmed.2.fastq

Error message returned from bmtagger :

bmtagger: unrecognized option `--extract'

I did not set up that parameter, where does this come from?

Thank you

Yang

[Lauren McIver]

Hi Yang, The "--extract" option is set by default in kneaddata. I wonder if you have an older or newer version of bmtagger then that used to test kneaddata as it looks like this option is no longer available in your bmtagger install. Can you send the bmtagger version you are using or share your install method? The bmtagger version we have been using is v1.1.0.  

Thanks,

Lauren

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